BACKGROUND Because of atypical clinical symptoms, lymphoma is easily confused with infectious diseases. Extranodal nasal-type natural killer/T-cell lymphoma (NKTL) is more common, and there are few cases of eyelid site onset and intracranial infiltration, which increases the difficulty of diagnosis. This disease usually has a very poor prognosis and there are few reports of recovery. CASE SUMMARY A 3-year-old boy was admitted to our hospital due to an initial misdiagnosis of "eyelid cellulitis" and failed antibiotic treatment. He was characterized by fever, right eyeball bulging, convulsions, and abnormal liver function. His blood Epstein-Barr virus (EBV) DNA was positive (8.798 x 10(4) copies/mL), and remained positive for about half a year. The cranial imaging examination suggested a space-occupying lesion in the right eyelid, with the right temporal lobe and meninges involved. The boy underwent ocular mass resection. The pathological diagnosis was NKTL. He was diagnosed as having NKTL with intracranial infiltration, combined with chronic active EBV infection (CAEBV). Then he underwent systemic chemotherapy and intrathecal injection. The boy suffered from abnormal blood coagulation, oral mucositis, diarrhea, liver damage, and severe bone marrow suppression but survived. Finally, the tumor was completely relieved and his blood EBV-DNA level turned negative. The current follow-up has been more than 2 years and his condition is stable. CONCLUSION This case suggests that chemotherapy combined with intrathecal injection may have a good effect on intracranial infiltrating lymphoma and CAEBV, which deserves further study and discussion.